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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Pipeline version
        v1.0.0
        Contact E-mail
        qtl7@cdc.gov
        Project Type
        HMAS tripod analysis

        Report generated on 2024-09-07, 00:04 EDT based on data in:

        quast_report

        Assembly Statistics using Quast.

        Showing 80/80 rows and 4/4 columns.
        Sample NameN50 (Kbp)# of contigs >= 1KbpLargest contig (Kbp)Length (Kbp)
        CIMS-MN-055-SH-K-E_assembled
        282.8
        		49
        821.2
        		5038.7
        CIMS-MN-055-SH-M-E_assembled
        282.8
        		49
        821.2
        		5038.7
        CIMS-MN-055-IW-M-E_assembled
        282.8
        		49
        821.2
        		5038.7
        CIMS-MN-053-SH-K-E_assembled
        490.5
        		21
        1508.5
        		4738.2
        CIMS-MN-053-IW-K-E_assembled
        490.5
        		21
        1508.5
        		4738.2
        CIMS-MN-068-IW-M-E_assembled
        186.0
        		59
        514.5
        		5045.0
        CIMS-MN-068-SH-M-E_assembled
        186.0
        		59
        514.5
        		5045.0
        CIMS-MN-069-SH-M-E_assembled
        729.1
        		23
        1284.5
        		4937.2
        CIMS-MN-069-IW-M-E_assembled
        729.1
        		23
        1284.5
        		4937.2
        CIMS-MN-050-SH-K-E_assembled
        146.8
        		63
        396.3
        		5187.5
        CIMS-MN-067-SH-K-E_assembled
        490.3
        		20
        1508.5
        		4702.8
        CIMS-MN-058-SH-K-E_assembled
        561.2
        		21
        815.6
        		4714.6
        CIMS-MN-065-IW-K-E_assembled
        762.6
        		17
        2005.4
        		4712.3
        CIMS-MN-050-SH-M-E_assembled
        146.8
        		63
        396.3
        		5187.5
        CIMS-MN-056-IW-M-E_assembled
        434.4
        		23
        651.0
        		4823.7
        CIMS-MN-056-IW-K-E_assembled
        434.4
        		23
        651.0
        		4823.7
        CIMS-MN-050-IW-K-E_assembled
        146.8
        		63
        396.3
        		5187.5
        CIMS-MN-064-SH-M-E_assembled
        479.0
        		23
        938.4
        		4738.6
        CIMS-MN-065-SH-K-E_assembled
        762.6
        		17
        2005.4
        		4712.3
        CIMS-MN-065-SH-M-E_assembled
        762.6
        		17
        2005.4
        		4712.3
        CIMS-MN-064-SH-K-E_assembled
        479.0
        		23
        938.4
        		4738.6
        CIMS-MN-049-IW-K-E_assembled
        496.7
        		25
        1462.3
        		4788.4
        CIMS-MN-070-IW-M-E_assembled
        370.5
        		25
        1076.6
        		4685.7
        CIMS-MN-070-SH-M-E_assembled
        370.5
        		25
        1076.6
        		4685.7
        CIMS-MN-062-SH-K-E_assembled
        479.2
        		21
        1508.5
        		4705.7
        CIMS-MN-057-IW-M-E_assembled
        440.5
        		25
        1195.4
        		4655.9
        CIMS-MN-057-IW-K-E_assembled
        440.5
        		25
        1195.4
        		4655.9
        CIMS-MN-057-SH-M-E_assembled
        440.5
        		25
        1195.4
        		4655.9
        CIMS-MN-061-IW-M-E_assembled
        320.2
        		44
        820.8
        		4896.5
        CIMS-MN-059-IW-K-E_assembled
        490.5
        		20
        1508.5
        		4705.4
        CIMS-MN-059-IW-M-E_assembled
        490.5
        		20
        1508.5
        		4705.4
        CIMS-MN-059-SH-K-E_assembled
        490.5
        		20
        1508.5
        		4705.4
        CIMS-MN-051-IW-M-E_assembled
        433.3
        		21
        947.7
        		4663.0
        CIMS-MN-051-SH-M-E_assembled
        433.3
        		21
        947.7
        		4663.0
        CIMS-MN-050-IW-M-E_assembled
        146.8
        		63
        396.3
        		5187.5
        CIMS-MN-051-SH-K-E_assembled
        433.3
        		21
        947.7
        		4663.0
        CIMS-MN-055-IW-K-E_assembled
        282.8
        		49
        821.2
        		5038.7
        CIMS-MN-069-IW-K-E_assembled
        729.1
        		23
        1284.5
        		4937.2
        CIMS-MN-058-IW-K-E_assembled
        561.2
        		21
        815.6
        		4714.6
        CIMS-MN-069-SH-K-E_assembled
        729.1
        		23
        1284.5
        		4937.2
        CIMS-MN-067-IW-K-E_assembled
        490.3
        		20
        1508.5
        		4702.8
        CIMS-MN-065-IW-M-E_assembled
        762.6
        		17
        2005.4
        		4712.3
        CIMS-MN-056-SH-K-E_assembled
        434.4
        		23
        651.0
        		4823.7
        CIMS-MN-062-SH-M-E_assembled
        479.2
        		21
        1508.5
        		4705.7
        CIMS-MN-049-SH-K-E_assembled
        496.7
        		25
        1462.3
        		4788.4
        CIMS-MN-056-SH-M-E_assembled
        434.4
        		23
        651.0
        		4823.7
        CIMS-MN-064-IW-K-E_assembled
        479.0
        		23
        938.4
        		4738.6
        CIMS-MN-063-IW-M-E_assembled
        762.6
        		15
        2004.8
        		4711.1
        CIMS-MN-067-SH-M-E_assembled
        490.3
        		20
        1508.5
        		4702.8
        CIMS-MN-063-SH-K-E_assembled
        762.6
        		15
        2004.8
        		4711.1
        CIMS-MN-049-IW-M-E_assembled
        496.7
        		25
        1462.3
        		4788.4
        CIMS-MN-054-SH-K-E_assembled
        396.0
        		27
        659.2
        		4660.0
        CIMS-MN-053-SH-M-E_assembled
        490.5
        		21
        1508.5
        		4738.2
        CIMS-MN-054-IW-M-E_assembled
        396.0
        		27
        659.2
        		4660.0
        CIMS-MN-058-IW-M-E_assembled
        561.2
        		21
        815.6
        		4714.6
        CIMS-MN-060-IW-K-E_assembled
        376.8
        		32
        591.0
        		4916.5
        CIMS-MN-061-SH-K-E_assembled
        320.2
        		44
        820.8
        		4896.5
        CIMS-MN-061-SH-M-E_assembled
        320.2
        		44
        820.8
        		4896.5
        CIMS-MN-059-SH-M-E_assembled
        490.5
        		20
        1508.5
        		4705.4
        CIMS-MN-068-SH-K-E_assembled
        186.0
        		59
        514.5
        		5045.0
        CIMS-MN-063-SH-M-E_assembled
        762.6
        		15
        2004.8
        		4711.1
        CIMS-MN-060-SH-K-E_assembled
        376.8
        		32
        591.0
        		4916.5
        CIMS-MN-053-IW-M-E_assembled
        490.5
        		21
        1508.5
        		4738.2
        CIMS-MN-049-SH-M-E_assembled
        496.7
        		25
        1462.3
        		4788.4
        CIMS-MN-058-SH-M-E_assembled
        561.2
        		21
        815.6
        		4714.6
        CIMS-MN-054-IW-K-E_assembled
        396.0
        		27
        659.2
        		4660.0
        CIMS-MN-051-IW-K-E_assembled
        433.3
        		21
        947.7
        		4663.0
        CIMS-MN-061-IW-K-E_assembled
        320.2
        		44
        820.8
        		4896.5
        CIMS-MN-067-IW-M-E_assembled
        490.3
        		20
        1508.5
        		4702.8
        CIMS-MN-068-IW-K-E_assembled
        186.0
        		59
        514.5
        		5045.0
        CIMS-MN-062-IW-M-E_assembled
        479.2
        		21
        1508.5
        		4705.7
        CIMS-MN-064-IW-M-E_assembled
        479.0
        		23
        938.4
        		4738.6
        CIMS-MN-062-IW-K-E_assembled
        479.2
        		21
        1508.5
        		4705.7
        CIMS-MN-070-IW-K-E_assembled
        370.5
        		25
        1076.6
        		4685.7
        CIMS-MN-070-SH-K-E_assembled
        370.5
        		25
        1076.6
        		4685.7
        CIMS-MN-063-IW-K-E_assembled
        762.6
        		15
        2004.8
        		4711.1
        CIMS-MN-060-IW-M-E_assembled
        376.8
        		32
        591.0
        		4916.5
        CIMS-MN-060-SH-M-E_assembled
        376.8
        		32
        591.0
        		4916.5
        CIMS-MN-057-SH-K-E_assembled
        440.5
        		25
        1195.4
        		4655.9
        CIMS-MN-054-SH-M-E_assembled
        396.0
        		27
        659.2
        		4660.0

        tripod report

        Combined summary statistics for all the samples in the run, primer pairs (out of total 2461 in the Salmonella HMAS primer panel).

        Showing 46/46 rows and 4/4 columns.
        Sample Name# of FP# of not ident seqs# of matched most abund. seqs% of matched most abund. seqs
        CIMS-MN-108-MN-M05688-240618_S4720 0 / 20.000
        CIMS-MN-106-MN-M05688-240618_S2330 0 / 30.000
        CIMS-MN-105-MN-M05688-240618_S480 0 / 80.000
        CIMS-MN-080-IH-MN-M05688-240618_S2624430 0 / 24430.000
        CIMS-MN-063-IH-MN-M05688-240618_S1511217 2320 / 24490.947
        CIMS-MN-099-IH-MN-M05688-240618_S4524480 0 / 24480.000
        CIMS-MN-069-IH-MN-M05688-240618_S2111934 2296 / 24490.938
        CIMS-MN-058-IH-MN-M05688-240618_S1014328 2278 / 24490.930
        CIMS-MN-086-IH-MN-M05688-240618_S3224390 0 / 24390.000
        CIMS-MN-091-IH-MN-M05688-240618_S3724480 0 / 24480.000
        CIMS-MN-093-IH-MN-M05688-240618_S3924430 0 / 24430.000
        CIMS-MN-083-IH-MN-M05688-240618_S2924470 0 / 24470.000
        CIMS-MN-082-IH-MN-M05688-240618_S2824470 0 / 24470.000
        CIMS-MN-060-IH-MN-M05688-240618_S1211216 2322 / 24500.948
        CIMS-MN-068-IH-MN-M05688-240618_S2011720 2311 / 24480.944
        CIMS-MN-057-IH-MN-M05688-240618_S911217 2320 / 24490.947
        CIMS-MN-054-IH-MN-M05688-240618_S611636 2296 / 24480.938
        CIMS-MN-066-IH-MN-M05688-240618_S1824500 0 / 24500.000
        CIMS-MN-088-IH-MN-M05688-240618_S3424480 0 / 24480.000
        CIMS-MN-090-IH-MN-M05688-240618_S3624400 0 / 24400.000
        CIMS-MN-050-IH-MN-M05688-240618_S213431 2279 / 24440.932
        CIMS-MN-092-IH-MN-M05688-240618_S3824470 0 / 24470.000
        CIMS-MN-067-IH-MN-M05688-240618_S1911214 2322 / 24480.949
        CIMS-MN-085-IH-MN-M05688-240618_S3124490 0 / 24490.000
        CIMS-MN-061-IH-MN-M05688-240618_S1311218 2323 / 24530.947
        CIMS-MN-087-IH-MN-M05688-240618_S3324490 0 / 24490.000
        CIMS-MN-089-IH-MN-M05688-240618_S3524520 0 / 24520.000
        CIMS-MN-056-IH-MN-M05688-240618_S811726 2308 / 24510.942
        CIMS-MN-079-IH-MN-M05688-240618_S2524520 0 / 24520.000
        CIMS-MN-095-IH-MN-M05688-240618_S4124490 0 / 24490.000
        CIMS-MN-096-IH-MN-M05688-240618_S4224510 0 / 24510.000
        CIMS-MN-097-IH-MN-M05688-240618_S4324470 0 / 24470.000
        CIMS-MN-062-IH-MN-M05688-240618_S1411316 2322 / 24510.947
        CIMS-MN-098-IH-MN-M05688-240618_S4424510 0 / 24510.000
        CIMS-MN-081-IH-MN-M05688-240618_S2724500 0 / 24500.000
        CIMS-MN-053-IH-MN-M05688-240618_S511320 2318 / 24510.946
        CIMS-MN-064-IH-MN-M05688-240618_S1611317 2322 / 24520.947
        CIMS-MN-051-IH-MN-M05688-240618_S311915 2318 / 24520.945
        CIMS-MN-059-IH-MN-M05688-240618_S1111216 2323 / 24510.948
        CIMS-MN-065-IH-MN-M05688-240618_S1711315 2324 / 24520.948
        CIMS-MN-049-IH-MN-M05688-240618_S111318 2318 / 24490.947
        CIMS-MN-109-IH-MN-M05688-240618_S4824520 0 / 24520.000
        CIMS-MN-055-IH-MN-M05688-240618_S711317 2323 / 24530.947
        CIMS-MN-094-IH-MN-M05688-240618_S4024530 0 / 24530.000
        CIMS-MN-084-IH-MN-M05688-240618_S3024510 0 / 24510.000
        CIMS-MN-100-IH-MN-M05688-240618_S4624530 0 / 24530.000

        MultiQC v1.21 - Written by Phil Ewels, available on GitHub.

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